Abstract
Activating mutations in PTPN11, encoding the cytosolic protein tyrosine phosphatase SHP2, result in developmental disorders and act as oncogenic drivers in patients with hematologic cancers. The allosteric inhibitor SHP099 stabilizes the wild-type SHP2 enzyme in an autoinhibited conformation that is itself destabilized by oncogenic mutations. Here, we report the impact of the highly activated and most frequently observed mutation, E76K, on the structure of SHP2, and investigate the effect of E76K and other oncogenic mutations on allosteric inhibition by SHP099. SHP2E76K adopts an open conformation but can be restored to the closed, autoinhibited conformation, near-identical to the unoccupied wild-type enzyme, when complexed with SHP099. SHP099 inhibitory activity against oncogenic SHP2 variants in vitro and in cells scales inversely with the activating strength of the mutation, indicating that either oncoselective or vastly more potent inhibitors will be necessary to suppress oncogenic signaling by the most strongly activating SHP2 mutations in cancer.
Highlights
Activating mutations in PTPN11, encoding the cytosolic protein tyrosine phosphatase SHP2, result in developmental disorders and act as oncogenic drivers in patients with hematologic cancers
Amino acids of the SHP2 C-SH2 domain do not directly interact with either the N-SH2 or PTP domains, the orientation of the C-SH2 domain in the autoinhibited conformation of SHP2 is stabilized through interactions of the unstructured loop between N-SH2 and C-SH2 domains with N-SH2 and PTP domains and of the linker between C-SH2 and PTP domains with the PTP domain
In comparison with the basal conformation of SHP2WT, the C-SH2 domain of SHP2E76K undergoes a 120-degree rotation with respect to the adjacent PTP domain, which fully exposes the PTP active site and repositions the N-SH2 domain onto a PTP domain surface opposite the catalytic pocket
Summary
Activating mutations in PTPN11, encoding the cytosolic protein tyrosine phosphatase SHP2, result in developmental disorders and act as oncogenic drivers in patients with hematologic cancers. This class of allosteric inhibitors was designed to stabilize the autoinhibited state of the enzyme by acting as a molecular glue between the N-SH2 domain and the catalytic domain One such compound, SHP099, binds to wildtype SHP2 with nanomolar affinity in biochemical assays, and exhibits antiproliferative activity in cancer cell lines that are dependent on receptor tyrosine kinases and wild-type SHP28. A broad range of SHP2 oncogenic mutants can be inhibited by SHP099 in assays using the purified enzyme, the potency of inhibition scales inversely with the basal phosphatase activity of each variant, and in cells, the more active SHP2 oncoproteins display resistance to allosteric inhibition These data show that oncoselective SHP2 inhibitors, or vastly more potent allosteric inhibitors, will be necessary to suppress the aberrant signaling that results from strongly activating SHP2 mutations in cancer
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